Biology subjects

Zhang, K.

Publications and source records attributed to Zhang, K..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

RBMX2: A Pivotal Regulator Linking Mycobacterium bovis Infection to Epithelial-Mesenchymal Transition and Lung Cancer Progression

Tuberculosis (TB) is a complex disease that arises from the dynamic interplay among the pathogen, host, and environmental factors. In 2022, TB affected approximately 10.6 million people worldwide, resulting in 1.3 million deaths. In regions with a high burden of zoonotic TB, Mycobacterium bovis (M. bovis) accounts for nearly 10% of human TB cases. The immune evasion strategies and latent nature of Mycobacterium tuberculosis (M. tb) pose significant challenges to understanding the host immune response to TB infection. In this study, we identify RNA-binding motif protein X-linked 2 (RBMX2) as a novel host factor that may facilitate M. bovis infection. However, the molecular mechanisms and functional roles of RBMX2 during M. bovis infection remain poorly understood. Our findings show that RBMX2 is significantly upregulated across multiple cell types following infection, including embryonic bovine lung (EBL) cells, bovine macrophage (BoMac) cells, bovine pulmonary alveolar primary cells, and human alveolar epithelial cells (A549). Using a combination of global transcriptomic sequencing, proteomic profiling, cell adhesion assays, ChIP-PCR, and Western blotting, we demonstrate that RBMX2 suppresses cell adhesion and tight junction formation in EBL cells while promoting M. bovis adhesion and invasion through activation of the p65 signaling pathway. Importantly, integrated analyses of transcriptomic, proteomic, and metabolomic data reveal that RBMX2 plays a key role in regulating epithelial-mesenchymal transition (EMT), a cellular process closely associated with cancer progression. To further explore the potential link between RBMX2 and cancer, we analyzed the TIMER2.0 database and found elevated RBMX2 expression in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues compared to normal lung tissues. These findings were corroborated by immunofluorescence staining. Using an M. bovis-infected BoMac-induced EBL-EMT model, we show that RBMX2 promotes EMT through activation of the p65/MMP-9 pathway following infection. Additionally, we validated the EMT process in human lung epithelial cancer cells (H1299), further supporting the involvement of RBMX2 in this transition. Collectively, our study identifies RBMX2 as a novel host factor that may enhance M. bovis infection and drive infection-induced EMT. These findings provide new insights into the molecular mechanisms underlying TB pathogenesis and suggest that RBMX2 could serve as a potential target for the development of TB vaccines and therapeutic strategies against TB-associated lung cancer.

microbiology↗

bioRxiv2025

Identification of Monotonically Classifying Pairs of Genes for Ordinal Disease Outcomes

In this study, we extend an existing classification method for identifying pairs of genes whose joint expression is associated with binary outcomes to ordinal multi-class outcomes, such as overall survival or disease progression. Our approach is motivated by the need for interpretable classifiers that can provide insights into the underlying biological mechanisms. It can be easily adapted to different research questions, such as identifying gene pair signatures or functional enrichment. We demonstrate that our method is comparable to state-of-the-art classification approaches in terms of performance, while offering the benefit of higher interpretability and adaptability to solve different research questions. Our evaluation on two real-world use cases in glioblastoma and high-grade serous ovarian carcinoma shows that our approach can effectively predict ordinal outcomes and provide novel biological insights. The code is available at https://github.com/oceanefrqt/MBMC.

systems biology↗

bioRxiv2025

A Spatial Multi-Omic Framework Identifies Gliomas Permissive to TIL Expansion

Tumor-infiltrating lymphocyte (TIL) therapy is effective in several tumor types; however, its feasibility in immune subversive tumors like glioblastoma is unclear. We expanded TILs from glioblastoma specimens and observed marked variability in yield, composition, function, and TCR clonality. By interrogating TILs expanded ex vivo alongside their sourced glioma tissue, we sought to identify determinants of successful (TIL+) vs unsuccessful TIL expansion (TIL-). Expanded TILs were predominantly effector memory CD4 cells and exhibited oligoclonal TCR enrichment. Despite similar T cell abundance in TIL vs TIL- tumors, TIL tumors exhibited distinct spatial organization and cellular interactions, including increased endothelial-immune interactions/ proximity and enrichment of vascular-associated niches. CD4 T cells localized near CD68 macrophages in TIL tumors, while they were positioned near CD163 CD206 macrophages in TIL- tumors. Thus, TIL expansion and functionality are linked to spatial organization and myeloid context; these features may enable biomarker-driven stratification for future TIL therapy in gliomas.

cancer biology↗

bioRxiv2025

Deciphering the molecular mechanisms of FET fusion oncoprotein-DNA hollow co-condensates

Biomolecules such as nucleic acids and proteins can undergo liquid-liquid phase separation to form biomolecular condensates with diverse architectures. However, fundamental questions surrounding the biophysical principles that govern condensate architecture and their potential biotechnological applications remain unresolved. Here, we report that the FUS/EWS/TAF15 family fusion oncoprotein FUS-ERG forms hollow co-condensates with double-stranded DNA containing GGAA microsatellites. Through a combination of biochemical assays, super-resolution imaging, and mathematical modeling, we reveal that the interior surface of hollow co-condensates exhibits properties distinct from those of the external surface, a phenomenon we term nested asymmetric phase separation. Furthermore, we demonstrate that the self-organization and morphology control of FUS-ERG hollow co-condensates can be harnessed for DNA-based information manipulation, enabling targeted DNA deletion within dsDNA libraries and facilitating dynamic, hierarchical data selection. These findings provide critical insights into the biophysical mechanisms underlying multicomponent phase-separated cellular bodies and establish a foundation for leveraging condensate morphology in biotechnology.

biophysics↗

bioRxiv2025

Exogenous melatonin mitigates drought stress by promoting the living cortical area of roots in cotton

The root cortex plays a critical role in water absorption, influencing root function and metabolic activity. However, the effects of melatonin on root cortical cells and its role in drought resistance remain unclear. This study examines the impact of exogenous melatonin on the root cortex of cotton under drought stress, focusing on its relationship with water uptake and drought resilience. Cotton plants were treated with 8% PEG6000 for drought stress and 100 {micro}M melatonin by foliar application. The results demonstrated that melatonin application significantly increased the living cortical area of roots under drought stress, with notable increases of 26.34% and 59.00% at distances of 1 cm and 13 cm from the root tip, respectively. Melatonin also enhanced root cortical thickness, promoted osmotic regulation, increased respiratory enzyme activity, and improved water and nutrient uptake. Furthermore, melatonin application promoted both root and shoot growth. Notably, the living cortical area positively correlated with osmotic substance accumulation, root respiration, and absorption capacity under drought conditions. In conclusion, exogenous melatonin alleviates drought-induced damage by enhancing the living cortical area, optimizing osmotic regulation, and improving root absorption, thus promoting cotton growth and drought resistance. These findings highlight melatonin as a promising regulator for enhancing drought resistance. HighlightExogenous melatonin increases root cortical integrity of cotton roots under drought stress, improves the absorption of water and nutrients, promotes the growth of cotton, and enhances its drought resistance.

physiology↗

bioRxiv2025

Conditional Diffusion with Locality-Aware Modal Alignment for Generating Diverse Protein Conformational Ensembles

Recent advances in AI have enabled the accurate prediction of a single stable protein structure solely based on its amino acid sequence. However, capturing the complete conformational landscape of a protein and its dynamic flexibility remains challenging. In this work, we developed Modal-aligned conditional Diffusion (Mac-Diff), a score based diffusion model for generating the conformational ensembles for unseen proteins. Central to Mac-Diff is an innovative attention module that enforces a delicate, locality-aware alignment between the conditional view (protein sequence) and the target view (residue pair geometry) to compute highly contextualized features for effective structural denoising. Furthermore, Mac-Diff leverages semantically rich sequence embedding from Protein Language Models like ESM-2 in enforcing the protein sequence condition that captures evolutionary, structural and functional information. This compensates for protein structural heterogeneity more effectively than embeddings from structure prediction models that are possibly biased to the dominant conformation. Mac-Diff showed promising results in generating realistic and diverse protein structures. It successfully recovered conformational distributions of fast folding proteins, captured multiple meta-stable conformations that were only observed in long MD simulation trajectories and efficiently predicted alternative conformations for allosteric proteins. We believe that Mac-Diff offers a useful tool to improve understanding of protein dynamics and structural variability, with broad implications for structural biology, drug discovery, and protein engineering.

bioinformatics↗

bioRxiv2025

Virus-host interactome reveals host cellular pathways perturbed by tick-borne encephalitis virus infection

Tick-borne encephalitis virus (TBEV) poses an increasingly significant threat to public health. Here, we delved into the virus-host interactome and discovered that TBEV has a profound impact on multiple host cellular pathways. Viral pre-membrane protein (prM), non-structural proteins NS1, NS2B3, NS4A, and NS5 remodel the hosts innate immune responses. PrM and NS2B3 are involved in autophagy, NS4A is associated with neurodegenerative diseases, and NS5 participates in spliceosome dynamics, ribosomal biogenesis, cell cycle regulation, and DNA damage response. Notably, TBEV infection causes G0/G1 cell cycle arrest in host cells. NS5 interacts with histone acetyltransferase P300 to upregulate P16 expression, suppressing CDK4 and resulting in cell cycle arrest. Elevated P16 and reduced CDK4 levels were observed in TBEV-infected brain organoids. The P300 inhibitors and CDK4 agonist can reverse virus-induced cell cycle arrest and inhibit viral replication. Further analysis uncovered potential antiviral targets like KAT6A, XIAP, and RIOK1/BRD9. These findings provide valuable insights into TBEV pathogenicity and hold promise for antiviral drug development.

microbiology↗

bioRxiv2025

Lactate dehydrogenase is the Achilles' heel of Lyme disease bacterium Borreliella burgdorferi

As a zoonotic pathogen, the Lyme disease bacterium Borreliella burgdorferi has evolved unique metabolic pathways, some of which are specific and essential for its survival and thus present as ideal targets for developing new therapeutics. B. burgdorferi dispenses with the use of thiamin as a cofactor and relies on lactate dehydrogenase (BbLDH) to convert pyruvate to lactate for balancing NADH/NAD+ ratios. This report first demonstrates that BbLDH is a canonical LDH with some unique biochemical and structural features. A loss-of-function study then reveals that BbLDH is essential for B. burgdorferi survival and infectivity, highlighting its therapeutic potential. Drug screening identifies four previously unknown LDH inhibitors with minimal cytotoxicity, two of which inhibit B. burgdorferi growth. This study provides mechanistic insights into the function of BbLDH in the pathophysiology of B. burgdorferi and lays the groundwork for developing genus-specific metabolic inhibitors against B. burgdorferi and potentially other tick-borne pathogens as well.

microbiology↗

bioRxiv2025

Phage defense and genome editing using novel retrons sourced from isolated environmental bacteria

Retrons are bacterial immune systems that protect a bacterial population against phages by killing infected hosts. Retrons typically comprise a reverse transcriptase, a template noncoding RNA that is partially reverse transcribed into RT-DNA, and a toxic effector. The reverse transcriptase, noncoding RNA, and RT-DNA complex sequester the toxic effector until triggered by phage infection, at which point the toxin is released to induce cell death. Due to their ability to produce single-stranded DNA in vivo, retrons have also been engineered to produce donor templates for genome editing in both prokaryotes and eukaryotes. However, the current repertoire of experimentally characterized retrons is limited, with most retrons sourced from clinical and laboratory strains of bacteria. To better understand retron biology and natural diversity, and to expand the current toolbox of retron-based genome editors, we developed a pipeline to isolate retrons and their bacterial hosts from a variety of environmental samples. Here, we present six of these novel retrons, each isolated from a different host bacterium. We characterize the full operon of these retrons and test their ability to defend against a panel of E. coli phages. For two of these retrons, we further unravel their mechanism of defense by identifying the phage genes responsible for triggering abortive infection. Finally, we engineer these retrons for genome editing in E. coli, demonstrating their potential use in a biotechnological application.

microbiology↗

bioRxiv2025

Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA

The stability and function of biomolecules are directly influenced by their myriad interactions with water. In this study, we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule, the Tetrahymena ribozyme, determined at 2.2 and 2.3 [A] resolutions. By employing segmentation-guided water and ion modeling (SWIM), an approach combining resolvability and chemical parameters, we automatically modeled and cross-validated water molecules and Mg2+ ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics (MD), supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modeling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and MD simulations.

biophysics↗

bioRxiv2025

DNAHX: a novel, non-motile dynein heavy chain subfamily, identified by cryo-EM endogenously

Ciliogenesis and cilia motility rely on the coordinated actions of diverse dyneins, yet the complexity of these motor proteins in cilia has posed challenges for understanding their specific roles. Traditional evolutionary analyses often overlook key family members due to technical limitations. Here, we present a cryo-EM-based, bottom-up approach for large-scale, de novo protein identification and functional prediction of endogenous axonemal dynein complexes. This approach led to the identification of a novel dynein heavy chain subfamily (XP_041462850), designated as DNAHX, from sea urchin sperm. Phylogenetic analysis indicates that DNAHX branches from the outer-arm dynein alpha chain during evolution and is found in specific animal lineages with external fertilization. DNAHX contains multiple insertions throughout the protein, locking DNAHX permanently in a pre-powerstroke state. The AAA1 site exhibits poor conservation of essential ATPase motifs, consistent with DNAHXs non-motile nature. DNAHX also forms a heterodimeric dynein complex, which we named dynein-X, with another dynein heavy chain and accessory chains. Furthermore, a subset of dynein-X displays an autoinhibited phi particle conformation, potentially facilitating the intraflagellar transport of axonemal dyneins. Our discovery of the novel, non-motile dynein heavy chain and the dynein-X complex provides valuable insights into the evolution of dyneins and potentially their diverse cellular functions.

biophysics↗

bioRxiv2025

HeteroRepur: Efficient Modeling of Heterogeneous Disease Graph for Depression Drug Repurposing using Heterogeneous Graph Neural Networks

ObjectiveMajor Depressive Disorder (MDD) is one of the most prevalent psychiatric disorders, yet existing treatments often result in suboptimal responses and encounter high recurrence rate. Repositioning existing medications, which often significantly reduces the required time and budget, has been demonstrated to be a promising strategy for drug discovery of multiple central nervous system (CNS) disorders. However, an efficient modeling strategy of heterogeneous semantic information among biological networks has yet to be developed for drug repurposing. Material and MethodsIn this study, we proposed HeteroRepur, by integrating heterogeneous graph neural networks to learn interaction features of Depression Drug Repurposing Graph (DDRG) and then classify drugs. ResultsThe DDRG embeddings learned by HeteroRepur accurately capture graph information, including 89 types of interaction or associations among drugs, genes, pathways, and GOs, as well as disease genetic network of MDD. In drug classification task, HeteroRepur outperforms various baseline models, including existing graph neural network approaches that do not consider heterogeneous network information. Finally, HeteroRepur predicts new candidates for treating MDD, including CNS drugs that have the potential to be extended to MDD, and dietary supplements that might benefit depression patients by elevating essential nutrient levels. ConclusionHeteroRepur outperforms traditional graph-based approaches, and can be used to rank promising drugs among complex disease networks with heterogeneous topology.

bioinformatics↗

bioRxiv2025

AncestryHub: A web server for local ancestry analysis

SummaryAncestryHub is a web version of local ancestry analysis software. It contains four built-in software and a set of built-in population reference panels. AncestryHub will significantly reduce the efforts and requirements for the users on their personal computational skills and computational hardware environment for ancestry analysis. Availabilityhttps://www.ancestryhub.4dgenome.com Contact: lima@4dgenome.com

bioinformatics↗

bioRxiv2024

A nucleotide code governs Lis1's ability to relieve dynein autoinhibition

Dynein-1 is a microtubule motor responsible for the transport of cytoplasmic cargoes. Activation of motility requires it first overcome an autoinhibited state prior to its assembly with dynactin and a cargo adaptor. Studies suggest that Lis1 may relieve dyneins autoinhibited state. However, evidence for this mechanism is lacking. We first set out to determine the rules governing dynein-Lis1 binding, which reveals that their binding affinity is regulated by the nucleotide-bound states of each of three nucleotide-binding pockets within the dynein motor domain. We also find that distinct nucleotide codes coordinate dynein-Lis1 binding stoichiometry by impacting binding affinity at two different sites within the dynein motor domain. Electron microscopy reveals that a 1 Lis1:1 dynein complex directly promotes an open, uninhibited conformational state of dynein, whereas a 2:1 complex resembles the autoinhibited state. Cryo-EM analysis reveals the structural basis for Lis1 opening dynein relies on interactions with the linker domain.

biochemistry↗

bioRxiv2024

Nde1 Promotes Lis1 Binding to Full-Length Autoinhibited Human Dynein-1

Cytoplasmic dynein-1 (dynein) is the primary motor for the retrograde transport of intracellular cargoes along microtubules. The activation of the dynein transport machinery requires the opening of its autoinhibited Phi conformation by Lis1 and Nde1/Ndel1, but the underlying mechanism remains unclear. Using biochemical reconstitution and cryo-electron microscopy, we show that Nde1 significantly enhances Lis1 binding to autoinhibited dynein and facilitates the opening of Phi. We discover a key intermediate step in the dynein activation pathway where a single Lis1 dimer binds between the Phi-like (PhiL) motor rings of dynein. In this "PhiL-Lis1", Lis1 interacts with one of the motor domains through its canonical interaction sites at the AAA+ ring and stalk and binds to the newly identified AAA5, AAA6, and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the PhiL-Lis1 interface. This intermediate state is instantly and efficiently formed in the presence of Nde1, but Nde1 is not part of the PhiL-Lis1. These findings provide key insights into the mechanism of how Nde1 promotes the Lis1-mediated opening of Phi dynein.

biophysics↗

bioRxiv2024

Molecular basis for the assembly of the dynein transport machinery on microtubules

Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has been elusive. Here, we reveal detailed structural insights into microtubule-mediated DDA assembly using cryo-electron microscopy. We find that an adaptor-independent dynein- dynactin complex (DD) predominantly forms on microtubules in an intrinsic 2:1 stoichiometry, induced by spontaneous parallelization of dynein upon microtubule binding. Adaptors can squeeze in and exchange within the assembled microtubule-bound DD complex, which is enabled by relative rotations between dynein and dynactin, and further facilitated by dynein light intermediate chains that assist in an adaptor search mechanism. Our findings elucidate the dynamic adaptability of the dynein transport machinery, and reveal a new mode for assembly of the motile complex.

biochemistry↗

bioRxiv2024

A Palette of Bridged Bicycle-Strengthened Fluorophores

Organic fluorophores are the keystone of advanced biological imaging. The vast chemical space of fluorophores has been extensively explored in seek of molecules with ideal properties. However, within the current molecular constraints, there appears to be a trade-off between high brightness, robust photostability, and tunable biochemical properties. Herein we report a general strategy to systematically boost the performance of donor-acceptor-type fluorophores by leveraging SO2 and O-substituted azabicyclo[3.2.1] octane auxochromes. These bicyclic heterocycles give rise to a collection of Bridged dyes (BD) spanning the UV and visible range with top-notch quantum efficiencies, enhanced water solubility, and tunable cell-permeability. Notably, these azabicyclic fluorophores showed remarkable photostability than its tetramethyl or azatidine analogue, at the same time completely resistant to oxidative photobluing rendered by the Bredts rule. Functionalized BD dyes are tailored for applications in single-molecule imaging, super-resolution imaging (STED and SIM) in fixed or live mammalian cells and plant cells, and live zebrafish imaging or chemigenetic voltage imaging. Synergizing with advanced imaging methods, the bridge bicycle dyes represent a versatile palette for biological researches.

biophysics↗

bioRxiv2024

Spatially barcoding biochemical reactions using DNA nanostructures unveil a major contact mechanism in proximity labeling

Proximity labeling techniques like TurboID and APEX2 have become pivotal tools in spatial omics research for studying protein interactions. However, the biochemical mechanisms underlying these reactive species-mediated labelings, particularly the spatial patterns of labeling methods within the sub-m range, remain poorly understood. Here, we employed DNA nanostructure platforms to precisely measure the labeling radii of TurboID and APEX2 through in vitro assays. Our DNA nanoruler design enables the deployment of oligonucleotide-barcoded labeling targets with nanometer precision near the enzymes. By quantifying labeling yields using quantitative PCR and mapping them against target distances, we uncovered surprising insights into the labeling mechanisms. Contrary to the prevailing diffusive labeling model, our results demonstrate that TurboID primarily operates through contact-dependent labeling. Similarly, APEX2 shows high labeling efficiency within its direct contact range. In parallel, it exhibits a low-level diffusive labeling towards more distant phenols. These findings reframe our understanding in the mechanism of proximity labeling enzymes, at the same time highlight the potential of DNA nanotechnology in spatially profiling reactive species.

biochemistry↗